ENSG00000044115:+:5:138827514:138887642

1. Sequences

id gene transcript strand chrom startGR endGR length seq type
ENSG00000044115:+:5:138827514:138887642 ENSG00000044115 ENST00000627109 + 5 138827515 138887642 438 AAACAAAUCAUUGUGGACCCCUUGAGCUUCAGCGAGGAGCGCUUUAGGCCUUCCCUGGAGGAGCGUCUGGAAAGCAUCAUUAGUGGGGCUGCCUUGAUGGCCGACUCGUCCUGCACGCGUGAUGACCGUCGUGAGCGAAUUGUGGCAGAGUGUAAUGCUGUCCGCCAGGCCCUGCAGGACCUGCUUUCGGAGUACAUGGGCAAUGCUGGACGUAAAGAAAGAAGUGAUGCACUCAAUUCUGCAAUAGAUAAAAUGACCAAGAAGACCAGGGACUUGCGUAGACAGCUCCGCAAAGCUGUCAUGGACCACGUUUCAGAUUCUUUCCUGGAAACCAAUGUUCCACUUUUGGUAUUGAUUGAAGCUGCAAAGAAUGGAAAUGAGAAAGAAGUUAAGGAGUAUGCCCAAGUUUUCCGUGAACAUGCCAACAAAUUGAUUGAGAAACAAAUCAUUGUGGACCCCUUGAGCUUCAGCGAGGAGCGCUUUAGGCC circ
ENSG00000044115:+:5:138827514:138887642 ENSG00000044115 ENST00000627109 + 5 138827515 138887642 22 AAUUGAUUGAGAAACAAAUCAU bsj
ENSG00000044115:+:5:138827514:138887642 ENSG00000044115 ENST00000627109 + 5 138827315 138827524 210 CUUCCACUGCUUUCUUUGAGGAGUGAUCAACAGUAGGCCAUCUUCUGUGGGACAGCCCCUUACCUGCUAAGAAGUAUAACUUUCUUUCAGAUGUUGGAAUUUUUGUGUUAAAUCUUGAUAUUACUAAUAACACUUUUCUCACCUUGAAUAAAGAAGGGAACAGAGAUGAGUACUAACAUUCGGUAAUACUUUCUCUGCAGAAACAAAUCA ie_up
ENSG00000044115:+:5:138827514:138887642 ENSG00000044115 ENST00000627109 + 5 138887633 138887842 210 AUUGAUUGAGGUAAGUGAAUUAGCAGUUUCAUUGACUUGUAGGCAACUUGGUGAAGUGUGGUGAGUUUUAAUCACAUUAUUUAAUCAGUUAAAAUUUGUAAGGGCUCGCUUAACAUACAACAUGUCUGAGAUGAUAGUCUUUCAUUAUCACUUAACAUCUAAGGAAAACUACCAUUUUGGUCACUUUACAUUAACUAUGUACGUUAUUAA ie_down
  • Note:
    • id: unique identifier.
    • gene: represents the gene from which the circRNA arises.
    • transcript: transcript whose exon coordinates overlap with the detected back-spliced junction coordinate and used in the downstream analysis.
    • strand: is the strand from which the gene is transcribed.
    • chrom: is the chromosome from which the circRNA is derived.
    • startGR: is the 5’ coordinate of the genomic range from which the sequence are extracted.
    • endGR: is the 3’ coordinate of the genomic range from which the sequence are extracted.
    • length: length of the extracted sequences.
    • seq: sequence used in the downstream analysis.
    • type: type of sequences retrieved. If type = “circ” the sequences derive from the internal circRNA sequences. If type = “bsj” the sequences derive from the back spliced junctions (BSJ). If type = “ie_up” the Intron or Exon sequences derive from the up-stream of BSJ up to 210 bp. If type = “ie_down” the Intron or Exon sequences derive from the down-stream of BSJ up to 210 bp.

2. RNA Binding Proteins Analysis

RBP on full sequence

Plot

Spreadsheet

id foreground background foregroundNorm backgroundNorm log2FC motifF motifB
ZC3H10 6 1053 0.015981735 0.0015274610 3.387217 CAGCGA,GAGCGA,GAGCGC,GGAGCG CAGCGA,CAGCGC,CCAGCG,CGAGCG,GAGCGA,GAGCGC,GCAGCG,GGAGCG
ANKHD1 1 339 0.004566210 0.0004927293 3.212130 GACGUA AGACGA,AGACGU,GACGAA,GACGAU,GACGUA,GACGUU
SRSF11 3 688 0.009132420 0.0009985015 3.193161 AAGAAG AAGAAG
ERI1 2 632 0.006849315 0.0009173461 2.900422 UUCAGA,UUUCAG UUCAGA,UUUCAG
IFIH1 1 904 0.004566210 0.0013115296 1.799747 GGCCCU CCGCGG,CGCGGA,GCCGCG,GCGGAU,GGCCCU,GGCCGC,GGGCCG
TRA2A 13 6871 0.031963470 0.0099589296 1.682361 AAAGAA,AAGAAA,AAGAAG,AGAAAG,AGAAGA,GAAAGA AAAGAA,AAGAAA,AAGAAG,AAGAGG,AGAAAG,AGAAGA,AGAGGA,AGGAAG,GAAAGA,GAAGAA,GAAGAG,GAGGAA
SNRPB2 1 991 0.004566210 0.0014376103 1.667325 GUAUUG AUUGCA,GUAUUG,UAUUGC,UGCAGU,UUGCAG
HNRNPA3 3 2140 0.009132420 0.0031027457 1.557452 AAGGAG,AGGAGC AAGGAG,AGGAGC,CAAGGA,CCAAGG,GCCAAG,GGAGCC
TRA2B 11 7329 0.027397260 0.0106226650 1.366886 AAAGAA,AAGAAG,AAGAAU,AGAAGA,GAAAGA AAAGAA,AAGAAC,AAGAAG,AAGAAU,AAGGAA,AAUAAG,AGAAGA,AGAAGG,AGGAAA,AGGAAG,AUAAGA,GAAAGA,GAAGAA,GAAGGA,GAAUUA,GGAAGG,UAAGAA
PABPN1 1 1222 0.004566210 0.0017723764 1.365312 AGAAGA AAAAGA,AGAAGA
LIN28A 6 4315 0.015981735 0.0062547643 1.353397 AGGAGU,CGGAGU,GGAGGA,GGAGUA,UGGAGG AGGAGA,AGGAGU,CGGAGA,CGGAGG,CGGAGU,GGAGAA,GGAGAU,GGAGGA,GGAGGG,GGAGUA,UGGAGA,UGGAGG,UGGAGU
KHDRBS2 2 1858 0.006849315 0.0026940701 1.346172 AUAAAA,GAUAAA AAUAAA,AUAAAA,AUAAAC,GAUAAA,UUUUUU
PUM2 2 1890 0.006849315 0.0027404447 1.321550 GUACAU,UAGAUA GUAAAU,GUACAU,GUAGAU,GUAUAU,UAAAUA,UACAUA,UACAUC,UAGAUA,UAUAUA,UGUAAA,UGUACA,UGUAGA,UGUAUA
SSB 1 1260 0.004566210 0.0018274462 1.321168 UGCUGU CUGUUU,GCUGUU,UGCUGU,UGUUUU
RBM41 1 1318 0.004566210 0.0019115000 1.256292 UACAUG AUACAU,AUACUU,UACAUG,UACAUU,UACUUG,UACUUU,UUACAU,UUACUU
SNRPA 10 7380 0.025114155 0.0106965744 1.231352 ACCUGC,AUGCAC,AUGCUG,CCUGCU,GUAUGC,UCCUGC,UGCACG,UUCCUG,UUUCCU ACCUGC,AGCAGU,AGGAGA,AGUAGG,AGUAGU,AUACCU,AUGCAC,AUGCUG,AUUCCU,AUUGCA,CAGUAG,CCUGCU,CUGCUA,GAGCAG,GAUACC,GAUUCC,GCAGUA,GGAGAU,GGGUAU,GGUAUG,GUAGGC,GUAGGG,GUAGUC,GUAGUG,GUAUGC,GUUACC,GUUUCC,UACCUG,UAUGCU,UCCUGC,UGCACA,UGCACC,UGCACG,UUACCU,UUCCUG,UUGCAC,UUUCCU
PUM1 7 5823 0.018264840 0.0084401638 1.113726 AAUGUU,AAUUGU,AGAUAA,GAAUUG,GUACAU,UAGAUA,UGUAAU AAUAUU,AAUGUU,AAUUGU,ACAUAA,AGAAUU,AGAUAA,AUUGUA,CAGAAU,CCAGAA,CUUGUA,GAAUUG,GUAAAU,GUAAUA,GUACAU,GUAGAU,GUAUAU,GUCCAG,UAAAUA,UAAUAU,UAAUGU,UACAUA,UACAUC,UAGAUA,UAUAUA,UGUAAA,UGUAAU,UGUACA,UGUAGA,UGUAUA,UGUCCA,UUAAUG,UUGUAC,UUGUAG,UUUAAU
U2AF2 1 1477 0.004566210 0.0021419234 1.092090 UUUUCC UUUUCC,UUUUUC,UUUUUU
SRSF4 4 3740 0.011415525 0.0054214720 1.074241 AAGAAG,AGAAGA AAGAAG,AGAAGA,AGGAAG,GAAGAA,GAGGAA,GGAAGA
CELF6 3 2997 0.009132420 0.0043447134 1.071736 GUGAUG,GUGGGG GUGAGG,GUGAUG,GUGGGG,GUGGUG,GUGUGG,GUGUUG,UGUGAG,UGUGAU,UGUGGG,UGUGGU,UGUGUG,UGUGUU
RBM24 2 2357 0.006849315 0.0034172229 1.003135 AGAGUG,GAGUGU AGAGUG,AGUGUG,GAGUGA,GAGUGG,GAGUGU,GUGUGA,GUGUGG,GUGUGU,UGAGUG,UGUGUG

RBP on BSJ (Exon Only)

Plot

Spreadsheet

id foreground background foregroundNorm backgroundNorm log2FC motifF motifB
SRSF9 1 134 0.09090909 0.008842023 3.361976 UGAGAA AGGAAA,AGGAAC,AGGACA,AGGACC,AGGAGA,AGGAGC,AUGAAC,AUGACA,AUGAGA,AUGAGC,CUGGAU,GAAGCA,GAAGCC,GAAGGA,GAAGGC,GAUGCA,GAUGCC,GAUGGA,GAUGGC,GGAAAA,GGAAAG,GGAACA,GGAACG,GGAAGC,GGAAGG,GGACAA,GGACAG,GGACCA,GGACCG,GGAGAA,GGAGAG,GGAGCA,GGAGCG,GGAGGA,GGAGGC,GGAUGG,GGGAGC,GGGUGG,GGUGCA,GGUGCC,GGUGGA,GGUGGC,UGAAAA,UGAACA,UGAACG,UGAAGC,UGAAGG,UGACAA,UGACAG,UGAGAA,UGAGAG,UGAGCA,UGAUGG,UGGAGC,UGGAGG,UGGUGC
SRSF10 1 160 0.09090909 0.010544931 3.107875 GAGAAA AAAAGA,AAAGAA,AAAGAC,AAAGAG,AAAGGG,AAGAAA,AAGACA,AAGAGA,AAGAGG,AAGGAA,AAGGGA,AAGGGG,ACAAAG,AGACAA,AGAGAA,AGAGAC,AGAGAG,AGAGGA,AGAGGG,CAAAGA,GAAAGA,GACAAA,GAGAAA,GAGAAC,GAGAAG,GAGACA,GAGACC,GAGACG,GAGAGA,GAGAGC,GAGGAA,GAGGAG,GAGGGA,GAGGGG

RBP on BSJ (Exon and Intron)

Plot

Spreadsheet

id foreground background foregroundNorm backgroundNorm log2FC motifF motifB
SRSF11 2 82 0.007142857 0.0004181782 4.094312 AAGAAG AAGAAG
RBM42 1 103 0.004761905 0.0005239823 3.183949 AACUAC AACUAA,AACUAC,ACUAAG,ACUACG
MATR3 3 216 0.009523810 0.0010933091 3.122837 AAUCUU,AUCUUG,CAUCUU AAUCUU,AUCUUA,AUCUUG,CAUCUU
YBX2 3 263 0.009523810 0.0013301088 2.839994 AACAUC,ACAACA,ACAUCU AACAAC,AACAUC,ACAACA,ACAACG,ACAACU,ACAUCA,ACAUCG,ACAUCU
EIF4B 2 226 0.007142857 0.0011436921 2.642803 GUUGGA,UUGGAA CUCGGA,CUUGGA,GUCGGA,GUUGGA,UCGGAA,UCGGAC,UUGGAA,UUGGAC
ERI1 2 228 0.007142857 0.0011537686 2.630147 UUCAGA,UUUCAG UUCAGA,UUUCAG
AGO1 2 283 0.007142857 0.0014308746 2.319604 GAGGUA,UGAGGU AGGUAG,GAGGUA,GGUAGU,GUAGUA,UGAGGU
HNRNPA0 1 200 0.004761905 0.0010126965 2.233337 AGUAGG AAUUUA,AGAUAU,AGUAGG
RBM41 4 502 0.011904762 0.0025342604 2.231902 AUACUU,UACAUU,UACUUU,UUACAU AUACAU,AUACUU,UACAUG,UACAUU,UACUUG,UACUUU,UUACAU,UUACUU
HNRNPM 1 222 0.004761905 0.0011235389 2.083489 AAGGAA AAGGAA,GAAGGA,GGGGGG
QKI 7 904 0.019047619 0.0045596534 2.062615 ACUAAC,ACUAAU,AUCUAA,AUUAAC,CUAACA,UAAUCA AAUCAU,ACACAC,ACACUA,ACUAAC,ACUAAU,ACUCAU,ACUUAU,AUCAUA,AUCUAA,AUCUAC,AUUAAC,CACACU,CACUAA,CUAACA,CUAACC,CUAACG,CUAAUC,CUACUC,CUCAUA,UAACCU,UAAUCA,UACUCA,UCAUAU,UCUAAU,UCUACU
RBM28 2 340 0.007142857 0.0017180572 2.055723 AGUAGG,UGUAGG AGUAGA,AGUAGG,AGUAGU,GAGUAG,GUGUAG,UGUAGA,UGUAGG,UGUAGU
TUT1 1 230 0.004761905 0.0011638452 2.032640 AAUACU AAAUAC,AAUACU,AGAUAC,CAAUAC,CGAUAC,GAUACU
SNRNP70 1 253 0.004761905 0.0012797259 1.895704 GAUCAA AAUCAA,AUCAAG,AUUCAA,GAUCAA,GUUCAA,UUCAAG
ZCRB1 4 666 0.011904762 0.0033605401 1.824774 ACUUAA,AUUUAA,GAAUUA,GCUUAA AAUUAA,ACUUAA,AUUUAA,GAAUUA,GACUUA,GAUUAA,GAUUUA,GCUUAA,GGAUUA,GGCUUA,GGUUUA,GUUUAA
RBM3 3 541 0.009523810 0.0027307537 1.802240 AAAACU,AAACUA,AAUACU AAAACG,AAAACU,AAACGA,AAACUA,AAGACG,AAGACU,AAUACG,AAUACU,AGACGA,AGACUA,AUACGA,AUACUA,GAAACG,GAAACU,GAGACG,GAGACU,GAUACG,GAUACU
A1CF 3 598 0.009523810 0.0030179363 1.657976 AGUAUA,AUCAGU,UGAUCA AGUAUA,AUAAUU,AUCAGU,CAGUAU,GAUCAG,UAAUUA,UAAUUG,UCAGUA,UGAUCA,UUAAUU
PABPC3 1 310 0.004761905 0.0015669085 1.603618 GAAAAC AAAAAC,AAAACA,AAAACC,GAAAAC
RC3H1 3 631 0.009523810 0.0031841999 1.580608 CUUCUG,UCUGUG,UUCUGU CCCUUC,CCUUCU,CUUCUG,UCCCUU,UCUGUG,UUCUGU
TRA2B 8 1447 0.021428571 0.0072954454 1.554468 AAAGAA,AAGAAG,AAGGAA,AGAAGG,AGGAAA,GAAUUA,UAAGAA AAAGAA,AAGAAC,AAGAAG,AAGAAU,AAGGAA,AAUAAG,AGAAGA,AGAAGG,AGGAAA,AGGAAG,AUAAGA,GAAAGA,GAAGAA,GAAGGA,GAAUUA,GGAAGG,UAAGAA
SF1 7 1294 0.019047619 0.0065245869 1.545652 ACUAAC,ACUAAU,AUUAAC,CUAACA,UACUAA,UGCUAA ACAGAC,ACAGUC,ACCGAC,ACGAAC,ACUAAC,ACUAAG,ACUAAU,ACUAGC,ACUGAC,ACUUAU,AGUAAC,AGUAAG,AUACUA,AUUAAC,CACAGA,CACCGA,CACUGA,CAGUCA,CGCUGA,CUAACA,GACUAA,GCUAAC,GCUGAC,GCUGCC,UAACAA,UACGAA,UACUAA,UACUAG,UACUGA,UAGUAA,UAUACU,UGCUAA,UGCUGA,UGCUGC
PABPC1 7 1321 0.019047619 0.0066606207 1.515882 ACAAAU,ACUAAC,ACUAAU,CAAAUC,CUAACA,CUAAUA,GAAAAC AAAAAA,AAAAAC,ACAAAC,ACAAAU,ACGAAC,ACGAAU,ACUAAC,ACUAAU,AGAAAA,CAAACA,CAAACC,CAAAUA,CAAAUC,CGAACA,CGAACC,CGAAUA,CGAAUC,CUAACA,CUAACC,CUAAUA,CUAAUC,GAAAAA,GAAAAC
SNRPA 10 1947 0.026190476 0.0098145909 1.416042 ACCUGC,AGCAGU,AGUAGG,CAGUAG,CCUGCU,CUGCUA,GUAGGC,UACCUG,UUACCU ACCUGC,AGCAGU,AGGAGA,AGUAGG,AGUAGU,AUACCU,AUGCAC,AUGCUG,AUUCCU,AUUGCA,CAGUAG,CCUGCU,CUGCUA,GAGCAG,GAUACC,GAUUCC,GCAGUA,GGAGAU,GGGUAU,GGUAUG,GUAGGC,GUAGGG,GUAGUC,GUAGUG,GUAUGC,GUUACC,GUUUCC,UACCUG,UAUGCU,UCCUGC,UGCACA,UGCACC,UGCACG,UUACCU,UUCCUG,UUGCAC,UUUCCU
SRSF4 2 558 0.007142857 0.0028164047 1.342647 AAGAAG AAGAAG,AGAAGA,AGGAAG,GAAGAA,GAGGAA,GGAAGA
HNRNPLL 3 748 0.009523810 0.0037736800 1.335567 ACAUAC,CACUGC,CAUACA ACAAAC,ACACAC,ACACCA,ACAUAC,ACCACA,ACCGCA,ACGACA,ACUGCA,AGACGA,CAAACA,CACACA,CACACC,CACCAC,CACCGC,CACUGC,CAGACG,CAUACA,GACGAC,GCAAAC,GCACAC,GCAUAC
CELF6 5 1196 0.014285714 0.0060308343 1.244144 GUGGUG,GUGUGG,UGUGGG,UGUGGU,UGUGUU GUGAGG,GUGAUG,GUGGGG,GUGGUG,GUGUGG,GUGUUG,UGUGAG,UGUGAU,UGUGGG,UGUGGU,UGUGUG,UGUGUU
RBMX 5 1316 0.014285714 0.0066354293 1.106311 AAGAAG,AAGGAA,AAGUGU,AGAAGG AAGAAG,AAGGAA,AAGUAA,AAGUGU,ACCAAA,AGAAGG,AGGAAG,AGUAAC,AGUGUU,AUCAAA,AUCCCA,AUCCCC,GAAGGA,GGAAGG,GUAACA,UAACAA,UAAGAC,UCAAAA
RBM24 3 888 0.009523810 0.0044790407 1.088349 AGUGUG,GAGUGA,GUGUGG AGAGUG,AGUGUG,GAGUGA,GAGUGG,GAGUGU,GUGUGA,GUGUGG,GUGUGU,UGAGUG,UGUGUG
CELF5 2 669 0.007142857 0.0033756550 1.081334 GUGUGG,UGUGUU GUGUGG,GUGUGU,GUGUUG,GUGUUU,UGUGUG,UGUGUU

Help

  • Note:
    • foreground: number of motifs found in the foreground target sequences (e.g. predicted circRNAs).
    • background: number of motifs found in the background target sequences (e.g. randomly generated circRNAs).
    • foregroundNorm: number of motifs found in the foreground target sequences (+1) divided by the number (or length) of sequences analyzed.
    • backgroundNorm: number of motifs found in background target sequences (+1) divided by the number (or length) of sequences analyzed.
    • log2FC: log2 fold change calculated in this way (foregroundNorm)/(backgroundNorm).
    • motifF: motifs of the corresponding RBP found in the foreground sequences.
    • motifB: motifs of the corresponding RBP found in the background sequences.

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